Hi CoffeeCat,
I was in the same position as you last year. I knew I wanted to pursue the MD-PhD, but I thought I was a much stronger candidate for a PhD program.
When you apply to an MD-PhD program, you usually fill out two applications (1) regular MD application, and (2) MD-PhD application. At some places, these two applications are sent to the same address, and at others, to separate addresses.
Your application is reviewed by an MD admissions committee, and an MD-PhD admissions committe (not a PhD committee). Usually, the MD-PhD committee decides first whether to interview you, and if they invite you to interview, you automatically get an MD interview.
The same thing goes for interviews as well. You will be interviewed and considered for acceptance by an MD-PhD committee separately from the MD committee. In my experience, if the MD-PhD committee decides to admit you, you're in. I guess there are some cases in which the MD-PhD committee wants to accept an applicant, but the MD committee is uncertain about them. In that situation, the MD-PhD committee, or the director, lobbies for you. Take Northwestern, for example. The director told us that if there is a discrepancy in the MD-PhD and MD committee decisions, that they [the MD-PhD committee] will "fight like hell" for you.
So, what does this all mean for someone who is seemingly a "better" applicant for a PhD program? In my opinion, and experience, the people who have the most power (MD-PhD program director and committee members) over the decision to interview you and admit you, are looking most closely at your research experiences and letters of reference from research mentors.
I hope this helps rather than confusing you even more!
